Identification of nucleic acid sequences in living organisms including infectious agents is useful for the diagnosis, prevention, and treatment of many diseases. In many synthetic chemical probes, double-stranded DNA formed by the molecular recognitions of complementary sequences is the primary feature to be identified. In many of these assays, it is desirable to immobilize expensive and difficult to prepare nucleic acid sequences to solid surfaces in order to maximize the potential for reuse. However, verification of the specific placement of the sequences on a solid substrate array can be difficult. Thus, there is a need to develop improved methods of the detection of the placement of probes on an array.
Many probe assays utilize synthetically prepared nucleic acid sequences. Nucleic acid sequences are typically prepared by solid phase synthesis using phosphoramidite derivatives. Direct conjugation of DNA molecules to different materials, such as dyes, sugars, and peptides during solid phase synthesis has practical challenges. Often the material to be conjugated to DNA will be not compatible with the conditions used to synthetically produce DNA through phosphoramidite couplings. Some conventional postsynthetic bioconjugation protocols, including carboxyl-group activation with N-hydroxysuccinimide (NHS)/N,N′-dicyclohexylcarbodiimide (DCC) are at times inefficient, particularly in the case of conjugating dye molecules to DNA. Thus, there is a need to identify improved methods for making conjugates containing nucleic acid sequences compatible with solid-phase synthetic procedures.